X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=309ab4a09c712132617c1fab8bd96e7849f4643b;hb=3c5c4e255ee8c36feb9e97aebc4e792e6ff8c440;hp=5a1572c26f582a02ae82dcfb729d4be2068ec6f5;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 5a1572c..309ab4a 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,19 +1,20 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
+#include "mothur.h"
 #include "groupmap.h"
+#include "treemap.h"
 
 using namespace std;
 
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
+class Tree;
 class OrderVector;
 class InputData;
 class GroupMap;
+class TreeMap;
 class SAbundVector;
 
 class GlobalData {
@@ -24,12 +25,14 @@ public:
 	InputData* ginput;
 	OrderVector* gorder;
 	ListVector* glist;
+	vector<Tree*> gTree;
 	SharedListVector* gSharedList;
 	SAbundVector* sabund;
 	GroupMap* gGroupmap;
+	TreeMap* gTreemap;
 	string inputFileName, helpRequest, commandName;
 	bool allLines;
-	vector<string> singleEstimators, summaryEstimators, sharedEstimators, rareEstimators, sharedRareEstimators, sharedSummaryEstimators; //holds estimators to be used
+	vector<string>  Estimators, Groups; //holds estimators to be used
 	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
 	
@@ -42,6 +45,8 @@ public:
 	string getGroupFile();
 	string getOrderFile();
 	string getFastaFile();
+	string getTreeFile();
+	string getSharedFile();
 	string getCutOff();
 	string getFormat();
 	string getPrecision();
@@ -50,6 +55,10 @@ public:
 	string getIters();
 	string getJumble();
 	string getFreq();
+	string getAbund();
+	string getRandomTree();
+	string getGroups();
+
 	void setListFile(string);
 	void setPhylipFile(string);
 	void setColumnFile(string);
@@ -57,22 +66,23 @@ public:
 	void setRabundFile(string);
 	void setSabundFile(string);
 	void setFormat(string);
+	void setRandomTree(string);
+	void setGroups(string);
+	void setCalc(string);
 
 	
 	void setListVector(ListVector*);
 	void setSparseMatrix(SparseMatrix*);
 	void clear(); 
+	void clearLabels();
+	void clearAbund();
 	
 	void parseGlobalData(string, string);
-	void splitAtEquals(string&, string&);
-	void splitAtComma(string&, string&);
-	void splitAtDash(string&, vector<string>&);
-	void splitAtDash(string&, set<int>&);
-	void splitAtDash(string&, set<string>&);
-	
+		
 private:
-	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile,line, label;
-	string cutoff, format, precision, method, fileroot, iters, jumble, freq, single, rarefaction, shared, summary, sharedsummary, sharedrarefaction;
+	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
+	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund;
+
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor
 	void operator=( const GlobalData& ); // Disable assignment operator
@@ -80,9 +90,10 @@ private:
 	~GlobalData();
 	ListVector* gListVector;
 	SparseMatrix* gSparseMatrix;
+	void reset();	//clears all non filename parameters
+	
+	
 	
 };
 
-//**********************************************************************************************************************
-
 #endif